From: Martin Hansen <mail@...>
Date: 2010-09-01T20:35:52+09:00
Subject: Re: Speed issues iterating over chars

Thanks Robert,

The gsub solution seems to be reasonably efficient.

>  seq.gsub! /./ do |m|
>   scores[$`.length].ord - BASE_SOLEXA < cutoff ? m.downcase! : m
> end

But my original proposed naive loop is twice as fast:

> scores.each_char do |score|
>   seq[i] = seq[i].downcase if score.ord - BASE_SOLEXA <= cutoff
>   i += 1
> end

I dont really know how gsub and tr compares to the Perl equivalents 
speed wise - in Perl tr is precompiling a lookup table that is evil fast 
and the regex engine is also primed at compile time and runs extremely 
fast.

I suspect that you need some C extension to go faster than this, but I 
don't really want to spend the time on that. I was exploring Inline C 
but that appears very fragile - I cannot even get the example from the 
cookbook up and running under Ruby 191/192.

Looking at your last proposal I see three iterations where two are 
running narrow if loops. I have not testet it, but it looks suspicious.

It is a shame that Ruby does not have build in bitwise operators for the 
String class allowing C speed masking. I have tried to get on the core 
mailing list to post this as a feature suggestion, but the ML form is 
stuffed.


Cheers,


Martin
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